Merge e62bb45 into 265bbd8

.dockerignore

@@ -0,0 +1,12 @@
+alembic
+tests
+trailblazer.egg-info
+.pytest_cache
+.github
+.editorconfig
+.gitignore
+.gitlint.yaml
+.pre-commit-config.yaml
+.configs
+DEPLOYMENT.md
+

.github/workflows/production_install_clinical-db.yml

@@ -21,7 +21,7 @@ jobs:
 
     - name: Test install on clinical-db
       run: |
-        pip install pip==9.0.1
+        pip install pip==21.0.1
         pip install .
         pip check
     - name: Test install dev on clinical-db

.github/workflows/production_install_hasta.yml

@@ -21,7 +21,7 @@ jobs:
 
     - name: Test install on hasta
       run: |
-        pip install pip==18.1
+        pip install pip==21.0.1
         pip install .
         pip check
     - name: Test install dev on hasta

Dockerfile

@@ -0,0 +1,21 @@
+FROM python:3.7-slim
+
+ENV GUNICORN_WORKERS=1
+ENV GUNICORN_TREADS=1
+ENV GUNICORN_BIND="0.0.0.0:5000"
+ENV GUNICORN_TIMEOUT=400
+
+WORKDIR /home/src/app
+COPY . /home/src/app
+
+RUN pip install -r requirements.txt
+RUN pip install -e .
+
+
+CMD gunicorn \
+  --workers=$GUNICORN_WORKERS \
+  --bind=$GUNICORN_BIND \
+  --threads=$GUNICORN_TREADS \
+  --timeout=$GUNICORN_TIMEOUT \
+  trailblazer.server.app:app
+

README.md

@@ -1,9 +1,8 @@
 # Trailblazer [![Coverage Status][coveralls-image]][coveralls-url]
 
-### Automate, monitor, and simplify running the [MIP][mip] analysis pipeline
+### Monitor the progress of analysis workflows submitted to SLURM
 
 Trailblazer is a tool that aims to provide:
-
 - a Python interface to interact with MIP in an automated fashion
 - a limited command line interface to simplify running MIP using an opinionated setup
 

requirements.txt

@@ -15,7 +15,9 @@ Flask-SQLAlchemy==2.1
 Flask-CORS
 Flask-Reverse-Proxy
 google-auth
+gunicorn
 
 # misc
 pymysql
 python-dateutil
+cryptography

trailblazer/cli/core.py

@@ -1,7 +1,6 @@
 import logging
-
+import os
 import click
-import coloredlogs
 import ruamel.yaml
 from dateutil.parser import parse as parse_date
 
@@ -16,15 +15,14 @@
 @click.group()
 @click.option("-c", "--config", type=click.File())
 @click.option("-d", "--database", help="path/URI of the SQL database")
-@click.option("-l", "--log-level", default="INFO")
 @click.version_option(trailblazer.__version__, prog_name=trailblazer.__title__)
 @click.pass_context
-def base(context, config, database, log_level):
+def base(context, config, database):
     """Trailblazer - Monitor analyses"""
-    coloredlogs.install(level=log_level)
-
     context.obj = ruamel.yaml.safe_load(config) if config else {}
-    context.obj["database"] = database or context.obj.get("database")
+    context.obj["database"] = database or os.environ.get(
+        "SQLALCHEMY_DATABASE_URI", "sqlite:///:memory:"
+    )
     context.obj["trailblazer"] = Store(context.obj["database"])
 
 

trailblazer/server/api.py

@@ -1,9 +1,10 @@
 import datetime
+import os
+
 from dateutil.parser import parse as parse_datestr
 from flask import abort, g, Blueprint, jsonify, make_response, request
 from google.auth import jwt
 from typing import Dict
-import subprocess
 import multiprocessing
 
 from trailblazer.server.ext import store
@@ -24,6 +25,8 @@ def before_request():
     """Authentication that is run before processing requests to the application"""
     if request.method == "OPTIONS":
         return make_response(jsonify(ok=True), 204)
+    if os.environ.get("SCOPE") == "DEVELOPMENT":
+        return
     auth_header = request.headers.get("Authorization")
     if auth_header:
         jwt_token = auth_header.split("Bearer ")[-1]

trailblazer/server/app.py

@@ -1,21 +1,18 @@
 # -*- coding: utf-8 -*-
 import os
-
-import coloredlogs
 from flask import Flask
 from flask_cors import CORS
 from flask_reverse_proxy import FlaskReverseProxied
 
 from trailblazer.server import api, ext
 
-coloredlogs.install(level="INFO")
 app = Flask(__name__)
 
 SECRET_KEY = "unsafe!!!"
 TEMPLATES_AUTO_RELOAD = True
-SQLALCHEMY_DATABASE_URI = os.environ["SQLALCHEMY_DATABASE_URI"]
-SQLALCHEMY_POOL_RECYCLE = 7200
-SQLALCHEMY_TRACK_MODIFICATIONS = "FLASK_DEBUG" in os.environ
+SQLALCHEMY_DATABASE_URI = os.environ.get("SQLALCHEMY_DATABASE_URI", "sqlite:///:memory:")
+SQLALCHEMY_POOL_RECYCLE = os.environ.get("SQLALCHEMY_POOL_RECYCLE", 7200)
+SQLALCHEMY_TRACK_MODIFICATIONS = os.environ.get("FLASK_DEBUG", False)
 
 app.config.from_object(__name__)